Hotspots of dendritic spine turnover facilitates new spines and NN sparsity (Frank et al 2018)

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Accession:227087
Model for the following publication: Adam C. Frank, Shan Huang, Miou Zhou, Amos Gdalyahu, George Kastellakis, Panayiota Poirazi, Tawnie K. Silva, Ximiao Wen, Joshua T. Trachtenberg, and Alcino J. Silva Hotspots of Dendritic Spine Turnover Facilitate Learning-related Clustered Spine Addition and Network Sparsity
Reference:
1 . Frank AC, Huang S, Zhou M, Gdalyahu A, Kastellakis G, Silva TK, Lu E, Wen X, Poirazi P, Trachtenberg JT, Silva AJ (2018) Hotspots of dendritic spine turnover facilitate clustered spine addition and learning and memory. Nat Commun 9:422 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell; Connectionist Network;
Brain Region(s)/Organism:
Cell Type(s): Abstract integrate-and-fire leaky neuron with dendritic subunits;
Channel(s):
Gap Junctions:
Receptor(s): NMDA;
Gene(s):
Transmitter(s):
Simulation Environment: C or C++ program; MATLAB;
Model Concept(s): Active Dendrites; Synaptic Plasticity;
Implementer(s): Kastellakis, George [gkastel at gmail.com];
Search NeuronDB for information about:  NMDA;
/
tomodel
exportfig
.ignore
README.md *
.gitignore *
append_pdfs.m *
copyfig.m *
crop_borders.m *
eps2pdf.m *
export_fig.m *
fix_lines.m *
ghostscript.m *
im2gif.m *
isolate_axes.m *
LICENSE *
pdf2eps.m *
pdftops.m *
print2array.m *
print2eps.m *
read_write_entire_textfile.m *
user_string.m *
using_hg2.m *
                            
function varargout = pdftops(cmd)
%PDFTOPS  Calls a local pdftops executable with the input command
%
% Example:
%   [status result] = pdftops(cmd)
%
% Attempts to locate a pdftops executable, finally asking the user to
% specify the directory pdftops was installed into. The resulting path is
% stored for future reference.
% 
% Once found, the executable is called with the input command string.
%
% This function requires that you have pdftops (from the Xpdf package)
% installed on your system. You can download this from:
% http://www.foolabs.com/xpdf
%
% IN:
%   cmd - Command string to be passed into pdftops.
%
% OUT:
%   status - 0 iff command ran without problem.
%   result - Output from pdftops.

% Copyright: Oliver Woodford, 2009-2010

% Thanks to Jonas Dorn for the fix for the title of the uigetdir window on
% Mac OS.
% Thanks to Christoph Hertel for pointing out a bug in check_xpdf_path
% under linux.
% 23/01/2014 - Add full path to pdftops.txt in warning.

% Call pdftops
[varargout{1:nargout}] = system(sprintf('"%s" %s', xpdf_path, cmd));
end

function path_ = xpdf_path
% Return a valid path
% Start with the currently set path
path_ = user_string('pdftops');
% Check the path works
if check_xpdf_path(path_)
    return
end
% Check whether the binary is on the path
if ispc
    bin = 'pdftops.exe';
else
    bin = 'pdftops';
end
if check_store_xpdf_path(bin)
    path_ = bin;
    return
end
% Search the obvious places
if ispc
    path_ = 'C:\Program Files\xpdf\pdftops.exe';
else
    path_ = '/usr/local/bin/pdftops';
end
if check_store_xpdf_path(path_)
    return
end
% Ask the user to enter the path
while 1
    if strncmp(computer,'MAC',3) % Is a Mac
        % Give separate warning as the uigetdir dialogue box doesn't have a
        % title
        uiwait(warndlg('Pdftops not found. Please locate the program, or install xpdf-tools from http://users.phg-online.de/tk/MOSXS/.'))
    end
    base = uigetdir('/', 'Pdftops not found. Please locate the program.');
    if isequal(base, 0)
        % User hit cancel or closed window
        break;
    end
    base = [base filesep];
    bin_dir = {'', ['bin' filesep], ['lib' filesep]};
    for a = 1:numel(bin_dir)
        path_ = [base bin_dir{a} bin];
        if exist(path_, 'file') == 2
            break;
        end
    end
    if check_store_xpdf_path(path_)
        return
    end
end
error('pdftops executable not found.');
end

function good = check_store_xpdf_path(path_)
% Check the path is valid
good = check_xpdf_path(path_);
if ~good
    return
end
% Update the current default path to the path found
if ~user_string('pdftops', path_)
    warning('Path to pdftops executable could not be saved. Enter it manually in %s.', fullfile(fileparts(which('user_string.m')), '.ignore', 'pdftops.txt'));
    return
end
end

function good = check_xpdf_path(path_)
% Check the path is valid
[good, message] = system(sprintf('"%s" -h', path_));
% system returns good = 1 even when the command runs
% Look for something distinct in the help text
good = ~isempty(strfind(message, 'PostScript'));
end

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